Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-06-18 14:05:54 -0400 (Fri, 18 Jun 2021).

CHECK results for piano on nebbiolo1

To the developers/maintainers of the piano package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/piano.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1391/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
piano 2.8.0  (landing page)
Leif Varemo Wigge
Snapshot Date: 2021-06-17 06:50:12 -0400 (Thu, 17 Jun 2021)
URL: https://git.bioconductor.org/packages/piano
Branch: RELEASE_3_13
Last Commit: f9697f5
Last Changed Date: 2021-05-19 11:58:37 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: piano
Version: 2.8.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:piano.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings piano_2.8.0.tar.gz
StartedAt: 2021-06-17 13:02:29 -0400 (Thu, 17 Jun 2021)
EndedAt: 2021-06-17 13:04:23 -0400 (Thu, 17 Jun 2021)
EllapsedTime: 113.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: piano.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:piano.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings piano_2.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/piano.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘piano/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘piano’ version ‘2.8.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘piano’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... WARNING
Missing or unexported object: ‘rsbml::species’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Unknown packages ‘HTSanalyzeR’, ‘PGSEA’ in Rd xrefs
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/piano.Rcheck/00check.log’
for details.



Installation output

piano.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL piano
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘piano’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (piano)

Tests output


Example timings

piano.Rcheck/piano-Ex.timings

nameusersystemelapsed
GSAheatmap3.0790.0763.155
GSAsummaryTable2.5030.0122.516
consensusHeatmap1.2130.0281.241
consensusScores0.1100.0120.122
diffExp3.7430.1083.873
exploreGSAres3.0920.3043.396
extractFactors0.1810.0280.209
geneSetSummary2.6260.0042.630
loadGSC0.0130.0000.012
loadMAdata0.1890.0040.193
networkPlot3.1750.2163.390
networkPlot22.5060.0322.539
polarPlot0.3390.0200.359
runGSA2.4810.0002.481
runGSAhyper0.2000.0040.204
runQC0.330.020.35
writeFilesForKiwi0.1110.0040.116